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Use of Rolling Circle Amplification to Rapidly Identify Species of Cladophialophora Potentially Causing Human Infection

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Abstract

The genus Cladophialophora comprises etiologic agents of disease in immunocompetent patients, ranging from mild cutaneous colonization to cerebral encephalitis, in addition to saprobic species. Due to the high degree of phenotypic similarity between closely related species of the genus, identification problems are imminent. In the present study, we described rapid and sensitive rolling circle amplification (RCA) method based on species-specific padlock probes targeted for the internal transcribed spacer regions of rDNA. ITS regions of 12 Cladophialophora species were sequenced, and subsequently, 10 specific padlock probes were designed for the detection of single nucleotide polymorphisms. The majority of circularizable padlock probes were designed based on single nucleotide polymorphisms (SNPs), while for C. bantiana, C. immunda and C. devriesii were characterized by two or more nucleotides. Individual species-specific probes correctly identified in all ten Cladophialophora species correctly by visualization on 1.2 % agarose gels used to verify specificity of probe-template binding; no cross-reactivity was observed. Simplicity, sensitivity, robustness and low costs provide RCA a distinct place among isothermal techniques for DNA diagnostics. However, restriction and specificity and sensitivity should be lowered and increased, respectively, to be useful for a wide variety of clinical applications.

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References

  1. Badali H, Gueidan C, Najafzadeh MJ, Bonifaz A, van den Ende AH, de Hoog GS. Biodiversity of the genus Cladophialophora. Stud Mycol. 2008;61:175–91.

    Article  PubMed  CAS  Google Scholar 

  2. Revankar SG, Sutton DA. Melanized fungi in human disease. Clin Microbiol Rev. 2010;23:884–928.

    Article  PubMed  Google Scholar 

  3. Queiroz-Telles F, Esterre P, Perez-Blanco M, Vitale RG, Salgado CG, Bonifaz A. Chromoblastomycosis: an overview of clinical manifestations, diagnosis and treatment. Med Mycol. 2009;47:3–15.

    Article  PubMed  Google Scholar 

  4. Horre R, De Hoog GS. Primary cerebral infections by melanized fungi: a review. Stud Mycol. 1999;43:176–93.

    Google Scholar 

  5. De Hoog GS, Guarro J, Gene J, Figueras MJ, editors. Atlas of clinical fungi. 2nd ed. Utrecht/Reus: Centraalbureau voor Schimmelcultures/Universitat Rovira i Virgili; 2000.

    Google Scholar 

  6. Badali H, Carvalho VO, Vicente VA, Attili AD, Kwiatkowski IB, Van Den Ende AHG, et al. Cladophialophora saturnica sp. nov., a new opportunistic species of Chaetothyriales revealed using molecular data. Med Mycol. 2009;47:51–62.

    Article  PubMed  CAS  Google Scholar 

  7. De Hoog GS, Nishikaku AS, Fernandez Zeppenfeldt G, Padin-Gonzalez C, Burger E, Badali H, et al. Molecular analysis and pathogenicity of the Cladophialophora carrionii complex, with the description of a novel species. Stud Mycol. 2007;58:219–34.

    Article  PubMed  Google Scholar 

  8. Badali H, Prenafeta-Boldu FX, Guarro J, Klaassen CH, Meis JF, De Hoog GS. Cladophialophora psammophila, a novel species of Chaetothyriales with a potential use in the bioremediation of volatile aromatic hydrocarbons. Fungal Biol. 2011;115:1019–29.

    Article  PubMed  CAS  Google Scholar 

  9. Leaw SN, Chang HC, Sun HF, Barton R, Bouchara JP, Chang TC. Identification of medically important yeast species by sequence analysis of the internal transcribed spacer regions. J Clin Microbiol. 2006;44:693–9.

    Article  PubMed  CAS  Google Scholar 

  10. Nilsson M. Lock and roll: single-molecule genotyping in situ using padlock probes and rolling circle amplification. Histochem Cell Biol. 2006;126:159–64.

    Article  PubMed  CAS  Google Scholar 

  11. Zeng JS, Sutton DA, Fothergill AW, Rinaldi MG, Harrak MJ, de Hoog GS. Spectrum of clinically relevant Exophiala species in the U.S.A. J Clin Microbiol. 2007;45:3713–20.

    Article  PubMed  CAS  Google Scholar 

  12. Afsarian MH, Shokohi T, Arzanlou M, Taheri Sarvtin M, Badali H. Phaeohyphomycosis due dematiaceous fungi; a review of the literature. J Mazand Univ Med Sci. 2012;22:109–36.

    Google Scholar 

  13. Zhou X, Kong F, Sorrell TC, Wang H, Duan Y, Chen SC. Practical method for detection and identification of Candida, Aspergillus, and Scedosporium spp. by use of rolling circle amplification. J Clin Microbiol. 2008;46:2423–7.

    Article  PubMed  CAS  Google Scholar 

  14. Lian X, De Hoog GS. Indoor wet cells harbour melanized agents of cutaneous infection. Med Mycol. 2010;48:622–8.

    Article  CAS  Google Scholar 

  15. Fire A, Xu SQ. Rolling replication of short DNA circles. Proc Natl Acad Sci USA. 1995;92:4641–5.

    Article  PubMed  CAS  Google Scholar 

  16. Liu D, Daubendiek SL, Zillman MA, Ryan K, Kool ET. Rolling circle DNA synthesis: small circular oligonucleotides as efficient templates for DNA polymerases. J Am Chem Soc. 1996;118:1587–94.

    Article  PubMed  CAS  Google Scholar 

  17. Kong F, Tong Z, Chen X, Sorrell T, Wang B, Wu Q, et al. Rapid identification and differentiation of Trichophyton species, based on sequence polymorphisms of the ribosomal internal transcribed spacer regions, by rolling-circle amplification. J Clin Microbiol. 2008;46:1192–9.

    Article  PubMed  CAS  Google Scholar 

  18. Kaocharoen S, Wang B, Tsui KM, Trilles L, Kong F, Meyer W. Hyperbranched rolling circle amplification as a rapid and sensitive method for species identification within the Cryptococcus species complex. Electrophoresis. 2008;29:3183–91.

    PubMed  CAS  Google Scholar 

  19. Davari M, van Diepeningen AD, Babai-Ahari A, Arzanlou M, Najafzadeh MJ, van der Lee TA, et al. Rapid identification of Fusarium graminearum species complex using Rolling Circle Amplification (RCA). J Microbiol Methods. 2012;89:63–70.

    Article  PubMed  CAS  Google Scholar 

  20. Najafzadeh MJ, Sun J, Vicente VA, de Hoog GS. Rapid identification of fungal pathogens by rolling circle amplification using Fonsecaea as a model. Mycoses. 2011;54:577–82.

    Article  Google Scholar 

  21. Badali H, Nabili M. Molecular tools in medical mycology; Jundishapur J Microbiol. 2013;6(1):1–3.

    Article  Google Scholar 

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Acknowledgments

This study and the work of H. Badali and H. Hamzehei were financially supported by the Mazandaran University of Medical Sciences, Sari, Iran, and the Zanjan University of Medical Sciences, Zanjan, Iran, respectively, which we gratefully acknowledge.

Conflict of interest

The authors have no conflicts of interest. The authors alone are responsible for the content and writing of the paper.

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Authors and Affiliations

  1. Laboratory Research Center, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran

    Hossein Hamzehei

  2. Department of Medical Parasitology and Mycology, School of Allied Medicine, Tehran University of Medical Sciences, Tehran, Iran

    Seyed Amir Yazdanparast

  3. Student Research Center/Molecular and Cell Biology Research Center (MCBRC), School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran

    Mehrnaz Mohammad Davoudi

  4. Department of Medical Parasitology and Mycology, Kurdistan University of Medical Sciences, Sanandaj, Iran

    Sadegh Khodavaisy

  5. Department of Medical Mycology and Parasitology, School of public health, Tehran University of Medical Sciences, Tehran, Iran

    Sadegh Khodavaisy

  6. Department of Microbiology, Damghan Branch Islamic Azad University, Damghan, Iran

    Mitra Golehkheyli

  7. Department of Medical Mycology and Parasitology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran

    Saham Ansari & Hamid Badali

  8. Invasive Fungi Research Center (IFRC)/Molecular and Cell Biology Research Center (MCBRC), School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran

    Hamid Badali

  9. CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands

    G. S. de Hoog

Authors
  1. Hossein Hamzehei
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  2. Seyed Amir Yazdanparast
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  3. Mehrnaz Mohammad Davoudi
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  4. Sadegh Khodavaisy
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  5. Mitra Golehkheyli
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  6. Saham Ansari
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  7. G. S. de Hoog
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  8. Hamid Badali
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Corresponding author

Correspondence to Hamid Badali.

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Hamzehei, H., Yazdanparast, S.A., Mohammad Davoudi, M. et al. Use of Rolling Circle Amplification to Rapidly Identify Species of Cladophialophora Potentially Causing Human Infection. Mycopathologia 175, 431–438 (2013). https://doi.org/10.1007/s11046-013-9630-7

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  • DOI: https://doi.org/10.1007/s11046-013-9630-7

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